Variant report

Variant	rs636928
Chromosome Location	chr11:65093484-65093485
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:65092980..65094562-chr11:65096918..65099257,2	MCF-7	breast:
2	chr11:65085883..65088356-chr11:65092626..65095231,3	MCF-7	breast:
3	chr11:65080778..65084410-chr11:65089814..65094122,5	K562	blood:
4	chr11:65092421..65094699-chr11:65099687..65101394,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000149798	Chromatin interaction
ENSG00000133884	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1152611	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1195733	0.81[EUR][1000 genomes]
rs12269727	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1633466	0.82[EUR][1000 genomes]
rs1858783	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28781278	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2904966	0.97[ASN][1000 genomes]
rs2904986	0.86[EUR][1000 genomes]
rs3016000	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4149813	0.92[EUR][1000 genomes]
rs482842	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs487397	0.92[ASN][1000 genomes]
rs487568	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs487989	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs488289	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs499027	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs503277	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs506280	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs507005	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs509303	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs526502	0.84[EUR][1000 genomes]
rs542142	0.97[ASN][1000 genomes]
rs560097	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs592050	0.86[EUR][1000 genomes]
rs603286	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs611910	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs620427	0.94[ASN][1000 genomes]
rs626555	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs626802	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs630055	0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs650056	0.92[ASN][1000 genomes]
rs655433	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs667341	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs668735	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs673147	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs676114	0.97[ASN][1000 genomes]
rs676573	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs8638	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv526181	chr11:64638041-65257329	Flanking Active TSS Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1539 gene(s)	inside rSNPs	diseases
2	nsv832190	chr11:64978144-65127613	Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	esv2422285	chr11:65013294-65254540	Genic enhancers Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	474 gene(s)	inside rSNPs	diseases
4	nsv897715	chr11:65083491-65427346	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	984 gene(s)	inside rSNPs	diseases
5	nsv897716	chr11:65083491-65481166	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	999 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs636928	POLA2	cis	multi-tissue	Pritchard
rs636928	POLA2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:65083600-65096600	Weak transcription	Primary hematopoietic stem cells	blood
2	chr11:65083800-65096600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr11:65085000-65100800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr11:65085200-65097200	Weak transcription	Stomach Mucosa	stomach
5	chr11:65085200-65101000	Weak transcription	Fetal Kidney	kidney
6	chr11:65085400-65097000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr11:65085800-65101000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr11:65088800-65101000	Weak transcription	Right Atrium	heart
9	chr11:65089200-65101000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr11:65089400-65101200	Weak transcription	Small Intestine	intestine
11	chr11:65089600-65096800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr11:65089800-65094800	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr11:65089800-65097400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr11:65089800-65100800	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr11:65089800-65101000	Weak transcription	Liver	Liver
16	chr11:65089800-65101000	Weak transcription	Esophagus	oesophagus
17	chr11:65090000-65095800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr11:65090000-65096800	Weak transcription	HepG2	liver
19	chr11:65090000-65097000	Weak transcription	Brain Anterior Caudate	brain
20	chr11:65090000-65097200	Weak transcription	Brain Angular Gyrus	brain
21	chr11:65090000-65097200	Weak transcription	Stomach Smooth Muscle	stomach
22	chr11:65090000-65101000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr11:65090000-65101000	Weak transcription	Brain Substantia Nigra	brain
24	chr11:65090000-65101000	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr11:65090200-65096600	Weak transcription	Primary monocytes fromperipheralblood	blood
26	chr11:65090200-65096800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr11:65090200-65097000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr11:65090200-65097000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr11:65090200-65097000	Weak transcription	Colon Smooth Muscle	Colon
30	chr11:65090200-65097000	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr11:65090200-65097200	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr11:65090200-65097200	Weak transcription	Brain Hippocampus Middle	brain
33	chr11:65090200-65097200	Weak transcription	Fetal Brain Female	brain
34	chr11:65090200-65097400	Weak transcription	HUES6 Cell Line	embryonic stem cell
35	chr11:65090200-65100800	Weak transcription	Primary neutrophils fromperipheralblood	blood
36	chr11:65090200-65100800	Weak transcription	Colonic Mucosa	Colon
37	chr11:65090200-65101000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr11:65090200-65101000	Weak transcription	Fetal Lung	lung
39	chr11:65090200-65101000	Weak transcription	Rectal Smooth Muscle	rectum
40	chr11:65090400-65094000	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr11:65090400-65094600	Weak transcription	Duodenum Mucosa	Duodenum
42	chr11:65090400-65094800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr11:65090400-65094800	Weak transcription	Fetal Intestine Large	intestine
44	chr11:65090400-65095200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr11:65090400-65095400	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr11:65090400-65096800	Weak transcription	HUVEC	blood vessel
47	chr11:65090400-65096800	Weak transcription	K562	blood
48	chr11:65090400-65096800	Weak transcription	Monocytes-CD14+_RO01746	blood
49	chr11:65090400-65097000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr11:65090400-65097000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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